Uploading large quantity of files and folders to a library i

I am currently running Sitefinity 7.3 on a Windows 2012 system and for my current project i need to allow our documentation team to upload a series of interactive html5 based training videos into an document library which is attached to azure storage. The videos consist of around 1400 files across 16 folders up to 4 folders deep. Using sitefinity's built in uploader for libraries i have to manually go through and create all 16 sub libraries, then upload files 100 at a time which isn't realistic for a production situation. However i have uploaded a full video just for testing purposes and all works great. Now im just looking for help with a way to make the upload process simpler so i can put it into a production environment. 

 My first thought was to use the Sitefinity Desktop App since it allows you to upload large quantities of files and you can just drag a folder over so it will create all the sub directories. On a normal library this works fine but it doesn't work if the library is using an azure storage blob because the file name is removed when the file is uploaded and files just overwrite each other. I have reported this as a bug a while back here feedback.telerik.com/.../129212-sitefinity-desktop-application-upload-files-by-removing-the-name-in-azure-storage but i don't think they are still developing the desktop app so it will probably never get fixed. 

 To my knowledge i cant change the number of files the sitefinity uploader allows or upload folders containing files. Right now the only method i can think of to make this work is to create a custom uploaded widget or a desktop application that uploads via sf web services, but before i started down that path i was hoping to see if anyone else had run into similar issues and how they resolved it or if anyone has any other clever ideas. 

 Thanks